Guide to Publishing a Scientific Paper

Ann M. Körner

• Publisher: Routledge
• Year: 2008
• Print ISBN: 9780415452656
• eBook ISBN: 9781134054916
• Topic: Education
• Subtopic: Education General

"Guide to Publishing a Scientific Paper" provides researchers in every field of the biological, physical and medical sciences with all the information necessary to prepare, submit for publication, and revise a scientific paper.

The book includes details of every step in the process that is required for the publication of a scientific paper, for example,

• use of correct style and language
• choice of journal, use of the correct format, and adherence to journal guidelines
• submission of the manuscript in the appropriate format and with the appropriate cover letter and other materials
• the format for responses to reviewers' comments and resubmission of a revised manuscript

The advice provided conforms to the most up-to-date specifications and even the seasoned writer will learn how procedures have changed in recent years, in particular with regard to the electronic submission of manuscripts.

Every scientist who is preparing to write a paper should read this book before embarking on the preparation of a manuscript. This useful book also includes samples of letters to the Editor and responses to the Editor's comments and referees' criticism. In addition, as an Appendix, the book includes succinct advice on how to prepare an application for funding.

The author has edited more than 7,500 manuscripts over the past twenty years and is, consequently, very familiar with all of the most common mistakes. Her book provides invaluable and straightforward advice on how to avoid these mistakes.

Dr. Körner is a professional editor and writer. She has an undergraduate degree from the University of Cambridge and a doctorate in Molecular Biophysics and Biochemistry from Yale University.

Chapter 1
The publication of scientific papers

1.1 Why publish?

You may want to publish your research as part of your quest for fame and fortune or, at the very least, for tenure, but the only truly appropriate reason for publishing your research is to tell others about it. The purpose of your paper is to explain why you did a piece of work, how you did it, what you found, and what your findings might mean. The explanation of your methodology should be sufficiently detailed to allow the scientists in your field to repeat your work exactly, if they so choose. Your work is the foundation on which other researchers will base their future work and, as you must surely recognize, your work is based on the earlier research of others.

The publication of your work does allow you to lay claim to a particular discovery, which might be major or minor but is not, I hope, trivial, so that others will refer to your work and your contribution to the field as they continue to make progress in that field. Your contribution to the field might, in turn, bring you a modicum of fame and fortune but it is more likely that it will bring you a little closer to tenure or a promotion.

Many young scientists are under the illusion that the more papers they publish, the more they will impress the world in general and their senior colleagues in particular. A physician said to me once, “The content of my papers doesn’t matter. When I’m up for promotion, it’s only the number of papers that will count!” He was wrong, of course, because nobody who is in a position to make a decision about a scientist’s future is just going to count that person’s publications. If the people who are to decide on your next position or promotion are not experts in your field, you can be sure that they will ask several scientists in your field to comment on the significance and quality of your publications and, very probably, to rank you among your peers. Before you proceed any further, give some careful thought to the possibility that the work that you want to publish might not be as complete as it could be. If you plan to do a lengthy series of experiments over the course of a year or so, it might be better to wait until all the experiments are complete and then to write a major paper. Such a paper in a prestigious journal will count for far more than many short papers in journals that accept relatively brief communications. By contrast, if you have made a very interesting and unexpected discovery or developed a new method that will be of significant interest and assistance to your colleagues in the field, it might be better to publish a short paper or a “Letter to the Editor” right away. Now is the time to ask yourself whether you should postpone writing a paper and do some more experiments. The paper that you might write after such a delay might include an impressive amount of new information and some valuable new conclusions. It might be much better than a series of shorter papers that describe each small step along the pathway towards your final goal.

1.2 What should be published?

The only scientific research that should be published is research that is absolutely reproducible. Scientific “truths” are hard to come by and they tend to change over time. Reproducible results are the next best thing to scientific truths. The interpretation of results can mutate but, if results are reproducible, they can withstand changes in interpretation and remain both useful and relevant. Thus, before you consider publishing the results of your experiments, you need to be sure that you can reproduce them in your laboratory either exactly or, at least, within the limits of statistically acceptable fluctuations.

I am not going to discuss statistics in this book. There are many fine books about the statistical analysis of experimental results and in all likelihood you are familiar with the methods that are used in your field. However, you should bear in mind that reviewers of your manuscript will be looking carefully both to see how often you repeated your experiments and to determine how your results fluctuated when you did so. If the reviewers are not satisfied that your experiments are reproducible, they will not look kindly upon the conclusions that you draw from your results. Furthermore, if your arguments are based on differences between individual results and if these differences themselves are not statistically significant, you will also have a problem when your manuscript is reviewed. Do not start to write a paper until you are sure you can satisfy the reviewers in this regard. I once returned a manuscript in veterinary science to its author with the comment, “This manuscript is unpublishable. In your experiments, you used samples taken from only one single horse. When you have repeated your experiments with samples from several horses and shown that your results are reproducible, I shall be happy to edit a revised version of your manuscript.”

Before you start writing your paper, you also should consider how many people are likely to find your work interesting. If you are working in a very small field, it is likely that your colleagues and competitors all publish in the same journals and that these journals have a relatively small circulation. Consider whether it might be better to do some more experiments to produce a piece of work that might be of greater general interest and might, thus, be publishable in a journal with wider circulation.

1.3 Who should publish?

Most research is a collaborative effort by members of a team. Such a team might include a faculty member and a small number of post-doctoral fellows, graduate students, and technicians or it might include a supervisor plus junior and senior technicians. The names that eventually find themselves on the title page of a manuscript are those of all the members of the team who contributed to the research. The final responsibility for the manuscript generally rests with the most senior member of the team, who will approve the manuscript in its final form and submit it to a journal. Junior members of any team should not attempt to publish their results without the agreement and support of the most senior member. The person with the authority to publish results is the person who “owns” the results and that person can, in general, be recognized most easily as the person who was responsible for obtaining the funds that supported the research.

Supervisors and faculty members—let us refer to them collectively as advisors—understand that the junior members of any team need to learn how to write papers if they are to advance in their careers. However, the extent of the help provided to junior members of any team varies and only rarely does an advisor make any effort to provide his junior collaborators with specific training in writing papers. A junior scientist’s excitement, when he has produced publishable results for the first time in his career, is often replaced by apprehension when his advisor reacts by saying, “That’s great. Now write it up!” The advisor will then await the initial draft of the paper and, depending on how patient he is, he will either work closely with his junior collaborator to revise the draft, explaining all the changes that he is making, or he will throw up his hands, disappear into his office, and prepare a new manuscript in which his junior collaborator’s draft is barely recognizable.

When you “own” the research, either because you are the leader of the team and you obtained the necessary funding or because the “owner” of the research project agrees that the ideas and execution were yours alone, the responsibility for publishing your results is yours. It is your job to prepare the manuscript in its final form and to shepherd it through the publication process. It is also your job to make sure that everyone who has contributed to the research is properly recognized.

Before you start writing, it is a good idea to determine which members of your team will be co-authors and which will simply receive an acknowledgment at the end of the paper. The issue of authorship can cause serious conflicts and test friendships. It has even destroyed careers as, for example, when a department head at a major medical school insisted on having his name on a paper and then, when problems emerged about the research, it became apparent that he had not even read the manuscript.

Under optimum conditions, there should be no doubt as to who deserves to be listed as an author on a paper. The authors are those who contributed intellectually to the substance of the paper and/or who performed the experiments that are to be described in the paper. Nonetheless, even under such conditions, there can be serious squabbling about the order in which authors are listed on the title page of the manuscript. Sometimes this problem can be avoided by inclusion of a footnote that states, “The first two authors contributed equally to this work.” Nonetheless, two ambitious postdoctoral fellows, Dr. Smart and Dr. Brainy, might still quarrel with their advisor because they know that their paper will be cited by others as “Smart et al.” or “Brainy et al.” and not as “Smart, Brainy et al.” or “Brainy, Smart et al.”

If the head of your section, your department, or even your laboratory insists that her name be included in the list of authors, even though she contributed nothing to the research and, in addition, she dozed through the seminars and group meetings at which it was discussed, you should take the problem to her superior for resolution. Even though the senior scientist might “own” the research, she does not have the right to be listed as an author if she made no intellectual contribution to the research. All the authors whose names appear under the title of a paper must have participated in the research described in the paper and should be able to discuss it fully, to field questions about it, and to take public responsibility for it. If the head of your laboratory or section has not made any contribution to the work described in the paper, she should not be included as an author. You can and, indeed, you should mention her name in the Acknowledgments at the end of the paper but you are not obligated to include her as an author.

The order of authors should reflect the contribution of each author, with the name of the person who contributed the most, in terms of effort and ideas, coming first. If the head of the laboratory has supervised the research, he is considered the senior author and his name is usually listed last. Before you start writing your paper, make sure that all issues relating to authorship have been resolved. If you, as the senior author, find yourself in an intractable situation, with co-authors jockeying for position, you have two choices. You can say, “I’m the boss! My decision is final,” or you can say, “Since you cannot agree among yourselves, I shall write several short papers, which I shall send to mediocre journals, and you’ll each get your name on a mediocre paper.” The thought of their work being buried in a second-or third-rate journal should be enough to persuade the quarrelsome members of your team to settle their differences and reach a compromise.

1.4 Where should you publish?

1.4.1 General considerations

You should choose the journal to which you are going to submit your paper before you start to write it. Every journal has a different format, and every journal describes its individual formatting requirements in a section entitled “Instructions to Authors.” If you have chosen a target journal before you start writing, you can follow the specific instructions for contributions to that journal as you prepare your manuscript for submission.

Since your work follows and extends similar work in your field, you probably already know where research such as yours is published. You have used methods described in previously published papers and your working hypothesis is based on the conclusions that others have published. The papers to which you will refer in your paper were probably published in a relatively small number of journals and you should choose from among them, in particular, if you work in a very circumscribed field, such as, for example, clinical biomechanics or astroparticle physics. However, if your work is of high caliber and broader interest, you might try to publish in Science, Nature, or the Proceedings of the National Academy of Sciences of the United States of America (known to most scientists as “PNAS”), all three of which are read by scientists in a wide variety of disciplines. You should bear in mind, however, that the wider the readership of a particular journal, the harder it is to publish in that journal. For example, the editors of Science accept only about 10 percent of the papers submitted for review and they reject approximately 65 percent of all manuscripts that are submitted to Science within a mere week to ten days of receiving them. The figures for Nature are similar. In 2005, the editors of Nature received a total of 8,943 manuscripts, of which they published only 915, and they returned most of the papers that they rejected to the authors without review.

There are thousands and thousands of journals. The website of the Mulford Library of the Medical College of Ohio, http://mulford.meduohio.edu/instr/, provides links to the Instructions to Authors of 3,500 journals and those are only the journals that deal with the biological and medical sciences. There are also large numbers of journals that serve researchers in the physical sciences and a useful link to the Instructions to Authors of many of them is http://www-library.lbl.gov/library/public/tmLib/journals/LibJourInstr.htm. A similar site with links to chemistry journals is http://www.ch.cam.ac.uk/c2k/cj/ and a site with links specifically to journals in physics is http://info.ifpan.edu.pl/journal.html. Geologists can find a list of 3,000 journals, published worldwide, on the website of the American Geological Institute (http://www.agiweb.org/georef/about/serials.html), as well as a link to an abbreviated list of the 99 journals that the Institute considers to be “priority journals.”

You can, if you like, take comfort in the fact that, with so many journals published annually, you are bound to get your paper published somewhere. To some extent, you are right. The companies that publish journals want to make money. They make money by selling subscriptions to libraries and educational institutions. If they are to fill a certain number of issues every year, they need papers from people like you. However, in the first instance, you should aim high and try to publish your paper in the best possible journal in your field.

1.4.2 Specific considerations

There are two practical matters that you need to address in your choice of journal. Many journals now require electronic submission of manuscripts and the instructions for such submissions can be quite complicated, in particular, when Figures and Tables are part of the manuscript. Before you make the final choice of your journal, look carefully at the most recent issues and establish to your own satisfaction that your research is appropriate for the journal. Then study the Instructions to Authors carefully to make sure that you can submit your manuscript in the required format. Your study of the Instructions to Authors might lead you to a discovery that surprises you. The publishers of some journals make you pay for the privilege of having your manuscript appear in one of their journals! In 2007, the charges for publication in one particular journal were as follows:

• Electronic manuscript: $105 per page
• Paper manuscript: $150 per page
• Color Figure surcharge (for the print edition): $100 per page.

If you think these prices are astronomical, you are right. They were the prices for publishing in the Astronomical Journal! It pays, in this regard, to study butterflies instead of the stars. The Journal of the Lepidopterists’ Society charged only $50 per page and asked a mere $25 from those lepidopterists who are not associated with an academic institution. When page charges were introduced, there was much grumbling. Nevertheless, the practice is now widespread and generally accepted. You need to make sure that you have the funds to pay for publication of your work and also for the reprints (known in Britain as offprints) that you will want to send to your colleagues. The payment of page charges has led to a peculiarly amusing anomaly: papers that appear in journals with page charges are referred to legally as “advertisements.”

1.5 Manuscripts for biomedical journals

If you are planning to write a paper for a biomedical journal, it would be a good idea at this point to read the “Uniform Requirements for Manuscripts Submitted to Biomedical Journals” of the International Committee of Medical Journal Editors, which you can find on the internet at http://www.icmje.org/index.html. At this address on the internet, you will also find a link (http://www.icmje.org/sponsor.htm) to an article on “Sponsorship, Authorship, and Accountability” by the same committee, which you should read carefully if your research is sponsored by a “for profit” or commercial organization rather than a non-profit or government organization. You will find on this website a careful analysis of problems related to conflicts of interest and, if you have any doubts as to possible conflicts of interest between you and your research on the one hand and your source of funding on the other, you should address them now, before you proceed any further.

Chapter 2
Before you start writing

2.1 Instructions to Authors

Every journal that is published supplies specific Instructions to Authors. If every author followed these instructions when preparing a manuscript, there would be only a limited need for a book such as this one. Every journal has its own specific set of instructions and, even though the instructions for submissions to all the journals produced by a particular scientific publisher tend to be very similar, different publishers provide different instructions. Authors tend to get lazy or, perhaps, I should say that they get carried away with the idea of publishing their research and, as a result, they prepare their manuscripts according to some preconceived idea or on the basis of a manuscript that they have published previously. Careful preparation before starting to write will save you time and spare you frustration later on. In publishing, as in everything else in life, it pays to READ THE INSTRUCTIONS.

When you have chosen the journal in which you hope to publish your work, spend some time looking at the papers in several of the most recent issues to get an idea of the style and format of papers in the journal. No matter how original your research mig...

Table of contents

• Cover Page
• Title Page
• Copyright Page
• Acknowledgments
• The ten most common mistakes
• Introduction
• 1 The publication of scientific papers
• 2 Before you start writing
• 3 The title page
• 4 The Abstract or Summary
• 5 The Introduction
• 6 Materials and Methods
• 7 Human subjects
• 8 Results
• 9 Discussion
• 10 Acknowledgments
• 11 References and Notes
• 12 Figures and Figure Legends
• 13 Tables
• 14 Supplementary information
• 15 First letter to the editor of your target journal
• 16 Submission of your paper
• 17 Letter from the editor and your response
• 18 Second letter to the editor with responses to reviewers
• 19 Congratulations, your paper has been accepted!
• Appendix. A note about writing applications for financial support
• Valedictory